Properties, Sequence, and Synthesis in Escherichia coli of 1-Aminocyclopropane-l-Carboxylate Deaminase from Hansenula saturnus

Matsuda, Rie; Uchiyama, Kyoko; Murakami, Tetuhide H.; Kawai, Jun; Mikami, Katsuhiro; Yamada, Takashi; Yokoi, Daisuke; Ito, Hiroyuki; Matsui, Hirokazu; Honma, Mamoru

doi:10.1093/oxfordjournals.jbchem.a022050

Cited by 85 publications

(40 citation statements)

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“…It has been previously suggested that the PLP-binding regions in these enzymes share the same fold, which consist of two domains (33). Some of the earliest descriptions of the structural attributes of yACCD based on a sequence comparison with TRPS␤ (16% identities in sequences) also suggested that the fold of yACCD would bare some similarity to that of TRPS␤ (11). On the other hand, the sequence comparisons of yACCD with TD and OASS detected (if any) very limited similarity (Fig.…”

Section: Resultsmentioning

confidence: 99%

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Crystal Structure of 1-Aminocyclopropane-1-carboxylate Deaminase from Hansenula saturnus

Yao¹,

Ose²,

Sugimoto³

et al. 2000

Journal of Biological Chemistry

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The pyridoxal 5-phosphate (PLP)-dependent enzyme 1-aminocyclopropane-1-carboxylate deaminase (ACCD) catalyzes a reaction that involves a ring opening of cyclopropanoid amino acid, yielding ␣-ketobutyrate and ammonia. Unlike other PLP-dependent enzymes, this enzyme has no ␣-hydrogen atom in the substrate. Thus, a unique mechanism for the bond cleavage is expected. The crystal structure of ACCD from Hansenula saturnus has been determined at 2.0 Å resolution by the multiple wavelength anomalous diffraction method using mercury atoms as anomalous scatterers. The model was built on the electron density map, which was obtained by the density averaging of multiple crystal forms. The final model was refined to an R-factor of 22.5% and an R free -factor of 26.8%. The ACCD folds into two domains, each of which has an open twisted ␣/␤ structure similar to the ␤-subunit of tryptophan synthase. However, in ACCD, unlike in other members of the ␤ family of PLPdependent enzymes, PLP is buried deep in the molecule. The structure provides the first view of the catalytic center of the cyclopropane ring opening.

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Section: Resultsmentioning

confidence: 99%

“…Crystallization and Data Collection-The yACCD was purified and crystallized as described previously (11,13). Mercury derivatives of yACCD were obtained by co-crystallization with 0.5 mM p-hydroxymercuribenzene sulfonate (PHMBS) using the hanging drop vapor diffusion method.…”

Section: Methodsmentioning

confidence: 99%

Crystal Structure of 1-Aminocyclopropane-1-carboxylate Deaminase from Hansenula saturnus

Yao¹,

Ose²,

Sugimoto³

et al. 2000

Journal of Biological Chemistry

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“…ACP and the yeast Cyberlindnera saturnus (previously Hansenula saturnus) were the two first microorganisms reported to synthesize ACC deaminase (Honma and Shimomura, 1978;Minami et al, 1998). Subsequently, ACC deaminase activity has been found in numerous bacteria, both gram positive and negative with a variety of different types of metabolism (for review, see Gamalero and Glick, 2012;Glick, 2014).…”

Section: Distribution and Phylogeny Of Acc Deaminasementioning

confidence: 99%

Bacterial Modulation of Plant Ethylene Levels

2015

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A focus on the mechanisms by which ACC deaminase-containing bacteria facilitate plant growth.Bacteria that produce the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase, when present either on the surface of plant roots (rhizospheric) or within plant tissues (endophytic), play an active role in modulating ethylene levels in plants. This enzyme activity facilitates plant growth especially in the presence of various environmental stresses. Thus, plant growth-promoting bacteria that express ACC deaminase activity protect plants from growth inhibition by flooding and anoxia, drought, high salt, the presence of fungal and bacterial pathogens, nematodes, and the presence of metals and organic contaminants. Bacteria that express ACC deaminase activity also decrease the rate of flower wilting, promote the rooting of cuttings, and facilitate the nodulation of legumes. Here, the mechanisms behind bacterial ACC deaminase facilitation of plant growth and development are discussed, and numerous examples of the use of bacteria with this activity are summarized.

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“…The gene encoding this enzyme has been isolated from a few strains of Pseudomonas spp., Rhizobium leguminosarum of the yeast Hansenula saturnus, and the fungus Penicillium citrinum. The crystal structure has been determined for the yeast (15) and bacterial (12) ACC deaminase enzymes; the biochemical and thermodynamic properties of the ACC deaminase from Pseudomonas putida UW4 have been measured (10). Here, using PCR with degenerate primers, we have successfully isolated ACC deaminase genes from a range of both gram-positive and gram-negative bacterial species.…”

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confidence: 99%

Evidence for Horizontal Transfer of 1-Aminocyclopropane-1-Carboxylate Deaminase Genes

Hontzeas

Richardson

Belimov

et al. 2005

Appl Environ Microbiol

121

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PCR was used to rapidly identify and isolate 1-aminocyclopropane-1-carboxylate (ACC) deaminase genes from bacteria. The Shimodaira-Hasegawa test was used to assess whether phylogenetically anomalous gene placements suggestive of horizontal gene transfer (HGT) were significantly favored over vertical transmission. The best maximum likelihood (ML) ACC deaminase tree was significantly more likely than four alternative ML trees, suggesting HGT.Plant growth-promoting bacteria include a diverse group of free-living soil bacteria that can stimulate the growth of plants by different direct or indirect mechanisms (5). Relatively recently, it was discovered that many plant growth-promoting bacteria contain the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase and that this enzyme can cleave the ethylene precursor ACC to ␣-ketobutyrate and ammonia and thereby lower the level of ethylene in developing or stressed plants (5,6,7,9,11,13). The gene encoding this enzyme has been isolated from a few strains of Pseudomonas spp., Rhizobium leguminosarum of the yeast Hansenula saturnus, and the fungus Penicillium citrinum. The crystal structure has been determined for the yeast (15) and bacterial (12) ACC deaminase enzymes; the biochemical and thermodynamic properties of the ACC deaminase from Pseudomonas putida UW4 have been measured (10). Here, using PCR with degenerate primers, we have successfully isolated ACC deaminase genes from a range of both gram-positive and gram-negative bacterial species. Using the biochemical assay procedure, it was ascertained that all of these putative genes encoded functional ACC deaminase. Furthermore, we propose that ACC deaminase genes did not evolve vertically but instead have undergone horizontal gene transfer (HGT).The bacterial strains used in this work are listed in Table 1. The bacteria, except for rhizobial strains, were routinely maintained on Bacto Pseudomonas F as described previously (1, 2, 3).For genus and species identification, a colony PCR was performed with live cells cultured on solid Bacto Pseudomonas F or M79 medium as described previously (17). Species assignment was confirmed by submitting the 16S rRNA sequences to the Ribosomal Database Project II (http://rdp.cme.msu.edu) and comparing them with their nearest phylogenetic relatives.Degenerate primers DegACC5Ј (5Ј-GGBGGVAAYAARM YVMGSAAGCTYGA) and DegACC3Ј (5Ј-TTDCCHKYRT ANACBGGRTC) were designed based upon stretches of conserved base pairs towards the N terminus of the protein and around the putative pyridoxal phosphate cofactor binding domain of the protein (20), whereas for 3Ј primer design, a conserved region close to the carboxyl terminus of the protein was utilized. This allows for the amplification of a fragment of approximately 750 bp. Thus, by using this PCR method, bacterial colonies can be quickly screened for the presence of the ACC deaminase gene. Nucleotide sequences were aligned using MUSCLE v3.52 (4, 16) and refined by eye. Phylogenetic analyses were performed using PAUP* v4.10b via an automated script (...

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Properties, Sequence, and Synthesis in Escherichia coli of 1-Aminocyclopropane-l-Carboxylate Deaminase from Hansenula saturnus

Cited by 85 publications

References 0 publications

Crystal Structure of 1-Aminocyclopropane-1-carboxylate Deaminase from Hansenula saturnus

Crystal Structure of 1-Aminocyclopropane-1-carboxylate Deaminase from Hansenula saturnus

Bacterial Modulation of Plant Ethylene Levels

Evidence for Horizontal Transfer of 1-Aminocyclopropane-1-Carboxylate Deaminase Genes

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